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Baker, Brett J

Brett J Baker

Assistant Professor
Department of Marine Science

Microbial diversity, ecology, and evolution - Tree of Life


Office Location

Postal Address


Ph.D., Earth and Environmental Sciences, University of Michigan, 2014

MS, Department of Biological Sciences, University of Wisconsin-Milwaukee, 2000

B.S., Biological Sciences, University of Wisconsin-Milwaukee, 1997


2015-present: Assistant Professor, Marine Science, Univ. of Texas Austin, Marine Science Institute

2014-2015: Senior Research Fellow, Marine Science, Univ. of Texas Austin, Marine Science Institute

2002-2010: Research Associate IV, Earth and Planetary Sciences, Univ. of California Berkeley

Microorganisms are key mediators in nearly all of the planet’s elemental cycles. However, our understanding of the ecological roles of many groups of microbes has been hampered by low-resolution analytical approaches to studying the staggering diversity present in nature. As a result the tree of life is full of branches, which remain undiscovered, and those, which have only been identified in single-gene sequencing surveys (Baker and Dick, 2013). This is a fundamental gap in our understanding of biology. Filling in the genomic gaps in the tree of life will provide a rich context to understand the evolution of life on the planet and will provide us with a genetic understanding of how microbial communities drive biogeochemical cycles.

Recent advances in DNA sequencing technologies and computational analyses have made it possible to reconstruct the genomes and transcriptomes of uncultured natural populations (Baker et al. 2010, 2012 and 2013). I have been involved in the development (Dick et al. 2009) and implementation of environmental omics since the beginning. I was involved in the first metaproteomic study of a microbial community (Ram et al. 2005) and have been using these approaches to track fine-scale evolutionary processes (Denef et al. 2010). Using these techniques I discovered deeply branching, novel groups of microbes (Archaea referred to as ARMAN) that are close to the predicted lower size limit of an organism (Baker et al. 2006). Obtaining complete genomes of the ARMAN phylum revealed that they have signatures of inter-species interactions and form connections to other species in nature (Baker et al. 2010).

More recently, my laboratory has reconstructed the genomes of hundreds of widespread, uncultured sediment microbes to understand how ecological roles are partitioned in these microbial communities. Many of the genomes belong to phyla which have no previous genomic representation and discovered three new groups of bacteria they play important roles in the global carbon cycle (Baker et al. 2015; Lazar, et al, Environ Micro). One of the new branches for which we have obtained several genomes for is a deeply branched member (Thorarchaeota) (Seitz et al. 2016). These genomes have provided rich insights into the evolutionary histories of life on the planet and we have been able to map the flow of carbon and energy, a microbial food web, through sediments with unprecedented detail (Baker et al. 2015).

SIGNIFICANT PUBLICATIONS (55 in total, google scholar

Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Seiber J, Teske AP, Ettema TJG, Baker BJ. (2019) New Asgard archaea capable of anaerobic hydrocarbon cycling. Nature Comm. 10, 1822.

Dombrowski N, Teske AP, Baker BJ. (2018) Extensive metabolic versatility and redundancy in microbial diverse, dynamic Guaymas Basin hydrothermal sediments. Nature Comm. 9, 4999.

Zaremba-Niedzwiedzka, K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, and Ettema TJG. (2017) Asgard archaea illuminates the origin of eukaryotic cellular complexity. Nature 541, 353-358.

Hug L, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle C, Butterfield CN, Hernsdorf AW, Amano Y, Suzuki Y, Dudek N, Relman DA, Thomas BC, Banfield JF (2016) A new view of the tree of life. Nature Microbiol. 1, 16048.

Dombrowski N, Donaho J, Teske AP, Gutierrez T, Seitz KW, Baker BJ. (2016) Hydrocarbon degradation pathways in uncultured bacteria from the Deep Water Horizon Oil Spill. Nature Microbiol. 1, 16057.

Baker BJ, Saw J, Lind A, Lazar CS, Hinrichs K-U, Teske AP, Ettema T (2016) Genomic inference of the metabolism of cosmopolitan subsurface archaea, Hadesarchaea. Nature Microbiol. 1, 16002.

Li M, Baker BJ, Anantharaman K, Breier J, Jain S, Dick GJ. (2015) Widespread uncultured deep-sea Archaea scavenge a variety of organic compounds. Nature Comm. 6, 8933.

Baker BJ, Lazar C, Dick GJ, Teske A. (2015) Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome, 3, 14.

Li M, Baker BJ, Anantharaman K, Breier J, Jain S, Dick GJ. (2015) Widespread uncultured deep-sea Archaea scavenge a variety of organic compounds. Nature Comm. 6, 8933.

Baker BJ, Comolli LR, Dick GJ, Hauser L., Land M, Hyatt, D, VerBerkmoes N, Hettich B, Banfield JF. (2010) Enigmatic, ultra-small uncultivated Archaea. Proc. Natl. Acad. Sci. 107, 8806-8811.

Dick GJ, Andersson, A, Baker BJ, Yelton P, Sheri SS, Thomas BC, Banfield JF. (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biology 10:R85.

Baker BJ, Tyson, GW, Webb RI, Flanagan J, Hugenholtz P, Banfield JF (2006) Lineages of acidophilic Archaea revealed by community genomic analysis. Science 314, 1933-1935.

Ram RJ, VerBerkmoes N, Thelen MP, Tyson GW, Baker BJ, Shah M, RC Blake II, Hettich R, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308, 1915-1920.

Sloan Foundation Fellowship in Ocean Sciences, 2016

Rackham Pre-doctoral Graduate Fellowship – 2013 competition, University of Michigan
               Funding for summer and fall 2013 through summer 2014

University of Texas College of Natural Science visualizing Science Contest 2015 – 1st place

“Using genomics to explore new branches on the tree of life” -
Invited speaker Geology Department, November 2018, Stanford University.
Invited speaker Ecology, Evolution and Marine Biology Department, April 2019, UC Santa Barbara

“Physiological capacity of archaea in anoxic sediments” -
EMBO Molecular biology of archaea: From mechanisms to ecology, Sept 5, Vienna, Austria

“The physiological capacity of novel microbes from marine sediments around the world” -
Gordon Research Conference – Marine Microbes, July 2, 2018, Lucca Italy

“Using metagenomics to explore new branches on the tree of life” -
Invited speaker in Biology Department, February 2018, Louisiana State University

“Resolving the roles of archaea in the early evolution of eukaryotes” -
Invited speaker in Integrative Biology January 2018, UT Austin

“Using metagenomics to explore new branches on the tree of life” -
Invited speaker Biochemistry Department, December 2017, Montana State University

“Using genomics to explore new branches on the tree of life” -
Invited speaker at Global Soil Biodiversity Conference GSBC2, October 2017, Nanjing, China

“Novel hydrocarbon pathways in sediment archaea” -
Keynote speaker at Goldschmidt Conference August 2017, Paris, France

“Illuminating the roles of uncultured sediment archaea in carbon and nitrogen cycling” -
Speaker at ASM Microbe conference, New Orleans, LA, June, 2017

“Exploring the unknown: Using genomic to explore new branches on the tree of life“ -
Presenter at Explore UT, a research presentation for the public Texas community

“Metagenomic explorations to new branches on the tree of life” -
Invited speaker for Darwin Day at University of Minnesota Duluth, Feb, 2017
Invited speaker at Texas A&M Univ., Feb 2017
Invited speaker at Oklahoma State Univ., March 2017

“Using metagenomics to illuminate the biology and ecology of new branches of microbial life” -
Invited seminar at Cal State San Bernardino, October 2016

“Resolving the ecological roles of novel and uncultured sediment archaea.” -
Keynote speaker at Extremophiles 2016 conference Kyoto Japan, Sept 2016

“How genomics is enlightening microbial biodiversity and ecology of marine sediments.” -
Invited speaker at JAMSTEC Yokohama Japan, Sept 2016

“Using omics to expand the tree of life and resolve ecological interactions” -
Invited speaker at Portland State Univ, Biology Dept, May 2016
Invited speaker at Oregon Health and Science Univ, May 2016

“Using omics to expand the tree of life and resolve ecological interactions” -
Invited speaker at Uppsala University, Sweden in June, 2016

“Everything we know is changing: How genomics is enlightening microbial biodiversity and ecology” -
Biology Dept seminar series, Texas A&M Corpus Christi, May, 2016

“Understanding microbial processes, dependencies and impacts through ‘omics” -
Convenor of session at AGU general meeting, San Francisco, December 2015

“Harnessing genomics to understand microbial biogeochemical cycling in estuary sediments” -
Invited speaker at University of Colorado Denver Integrative Biology Seminar, March 2015

“Resolving metabolic pathway and microorganisms involved in coastal petroleum degradation using high-resolution community omics approaches” -
Speaker at Gulf of Mexico Research Initiative Conference 2015, Houston, TX

“Harnessing community genomics to understand microbial iron and sulfur cycling in estuary sediments” -
Invited speaker American Chemical Society General Meeting, 2015, Denver CO

“Genomic Resolution of Linkages In Carbon, Nitrogen, And Sulfur Cycling Among Widespread and Novel Sediment Phyla” -
Speaker at ASM general meeting 2015, New Orleans, LA.

Aquatic microbial ecology, UT Spring 2016-present

Scientific communications, UT Spring 2017-present

Genomics in ocean science, UT Fall 2017-present